Sequence
atgc intronic sequence ATGC exonic sequence...tcatgtgaagtatggagtgttgtgctgtgctctaaagtggcaaaaacagtgccatttgagatagtttaatttttgtggcacaattaattgtttgttgcagTGAGTACTCGATGCAGCTGAATGCTTCTCGGATCAAAGTTCTTCAAGCTCAAGATGACGTGATCAGTTCCATGAAAGAAGCTGCATCCAAGGAACTGTTG
Basic information
species | Glycine max |
transcript | GLYMA05G37160.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G37160.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g46980.1 (Oryza sativa), 3'ss of exon 2
---tcatgtga-agtatggagtgttgtgctgtgctctaaagtggcaaaaacagtgccatttgagatagtttaatttttgtggcacaattaattgtttgttgcagTGAGTACTCGATGCAGCTGAATGCTTCTCGGATCAAAGTTCTTCAAGCTCAAGATGACGTGATCAGTTCCATGAAAGAAGCTGCATCCAAGGAACTGTTG
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tgattgcttgttagcatag-gtttcatagaatccacctgtatcactatttctgggtttatccatttg--ttaactgatgaggccttgttttctcctttat-cagTGAGTACTCTATGCAGCTGAATGCTTCTCGCATCAAAGTGCTTCAAGCTCAGGATGATTTGGTTAATTCCATGAAAGAGGATGCTACAAAGCAACTCCTG
upper sequence: GLYMA05G37160.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G030167_T01 (Zea mays), 3'ss of exon 2
---tcatgtgaagtatggagtgttgtgctgtgctctaaagtggcaaaaacagtgccatttgagatagtttaatttttgtggcacaattaattgtttgttg-cagTGAGTACTCGATGCAGCTGAATGCTTCTCGGATCAAAGTTCTTCAAGCTCAAGATGACGTGATCAGTTCCATGAAAGAAGCTGCATCCAAGGAACTGTTG
||||| | | || ||| | || | || ||| || ||| | | ||| | || | ||| ||||| |||||||||||| |||||| ||||||||||||| |||||||||||||||||||| ||||| | | | |||||||| | ||| |||||||| |
ccatcatggtttgcttt-agctttgagacatgtcattttgtatcaatgttcatgaattttcaaacctgtta---tctgacaagtttctgtttgcttgttaacagTGAGTACTCTATGCAGTTGAATGCTTCTCGCATCAAAGTTCTTCAAGCTCAGGATGATCTAGTTAACAAAATGAAAGACGATGCCATGAAGGAACTTCTC
upper sequence: GLYMA05G37160.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G070360_T01 (Zea mays), 3'ss of exon 2
--tcatgtgaagtatggagtgttgtgctgtgctctaaagtggcaaaaacagtgccatttgagatagtttaatttttgtggcacaattaattgtttgttg-cagTGAGTACTCGATGCAGCTGAATGCTTCTCGGATCAAAGTTCTTCAAGCTCAAGATGACGTGATCAGTTCCATGAAAGAAGCTGCATCCAAGGAACTGTTG
| | | | | | | | || | ||| || ||| | | ||| | || | || || | ||| |||||||||||| |||||| ||||||||||||| |||||||||||||||||||| ||||| | | | |||||||| | ||| |||||||| |
atttgctttatcttcgaggcataccattatgtcatgttacatcaatgtttatgatttttcaaacctgttatctaacaaggttctgtt---tgctcgttaacagTGAGTACTCTATGCAGTTGAATGCTTCTCGCATCAAAGTTCTTCAAGCTCAGGATGATCTAGTAAACAAAATGAAAGACGATGCGATGAAGGAACTCCTC
upper sequence: GLYMA05G37160.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G078839_T01 (Zea mays), 3'ss of exon 2
tcatgtgaagtatggagtgttgtgctgtgctctaaagtggcaaaaacagtgccatt--------tgagatagtttaattt--ttgtggcacaattaattgtttgttgcagTGAGTACTCGATGCAGCTGAATGCTTCTCGGATCAAAGTTCTTCAAGCTCAAGATGACGTGATCAGTTCCATGAAAGAAGCTGCATCCAAGGAACTGTTG
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----------tggatatttccccactttaccatatgctgatgaccatactgtttttcttttgtgtaaaacatatcaattcactgatcttattgtgtgtggtcttatgcagTGATTACTCGATGCAGCTCAATGCTTCCAGAATTAAAGTCCTTCAAGCTCAGGATGATTTGGTAACAGATATGTTGGAGTCAGCAAGGAAAGAGCTACTG
upper sequence: GLYMA05G37160.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G11150.1 (Arabidopsis thaliana), 3'ss of exon 2
---tcatgtgaagtatg-gagtgttgtgctgtgctctaaagtggcaaaaacagtgccatttgagatagtttaatttttgtggcacaattaattgt-ttgttgcagTGAGTACTCGATGCAGCTGAATGCTTCTCGGATCAAAGTTCTTCAAGCTCAAGATGACGTGATCAGTTCCATGAAAGAAGCTGCATCCAAGGAACTGTTG
| | | | || || || || || || || || || ||| || || || || | | | || || |||||| ||||| |||||||| ||||| || ||||||||||||||||||| ||||| || | ||| | |||||||||| ||| | ||||| || ||
atattgttagttctctgtgaaaattatgttgatctt----gtt-catttactgtgttatcgtgtattactttgccagaaaataactgtcatacatgttttttcagTGATTACTCTATGCAGCTAAATGCATCAAGGATCAAAGTTCTTCAAGCGCAAGACGATATTGTCAATGCCATGAAAGACCAAGCAGCTAAGGATCTTCTG
upper sequence: GLYMA05G37160.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv02s0025g01000.t01 (Vitis vinifera), 3'ss of exon 2
----tcatgtgaagtatggagtgttgtgctgtgctctaaagtggcaaaaacagtgccatttgagatagtttaatttttgtggcacaattaattgtttgttgcagTGAGTACTCGATGCAGCTGAATGCTTCTCGGATCAAAGTTCTTCAAGCTCAAGATGACGTGATCAGTTCCATGAAAGAAGCTGCATCCAAGGAACTGTTG
||| ||| ||| | || | | || || | ||| || || || | || | | | || | ||||||||||||| ||||| |||||||| ||||| |||||||| |||||||||||||||||||||||| | | || ||||||||||| |||||||| ||||| || ||
actgtcagaagaaaaatgaatcaatgccacacctttt----tgtcattactagtaatataggatctactgaaaaatgaaatgaatttatattgttttgttgcagTGAATACTCCATGCAGCTCAATGCCTCTCGGATTAAAGTTCTTCAAGCTCAAGATGACTTAGTTAGCTCCATGAAAGAGGCTGCATCGAAGGAGCTCCTG
upper sequence: GLYMA05G37160.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S68_127V6.1 (Physcomitrella patens), 3'ss of exon 2
tcatgtgaagtatggagtgttgtgctgtgctctaaag--tggcaaaaacagtgccatttgagatagtttaatttttgtggcacaattaattgtttgttgcagTGAGTACTCGATGCAGCTGAATGCTTCTCGGATCAAAGTTCTTCAAGCTCAAGATGACGTGATCAGTTCCATGAAAGAAGCTGCATCCAAGGAACTGTTG
| ||| | || | | | || | | | |||| | ||| || | | | | | |||| |||| ||||||||||||||| ||| |||||||||||||| | || | ||||||||||| |||||| || | | ||||||||||| || ||| | ||| |
-gaaacttagttcgaagaagtagctcctcatttagggcttaattataacatagtggtttctgagtatacatctgacttatggttttcaatt-tttggggcagTGAGTACTCGACGCAATTGAATGCTTCTCGGCTAAAGTTGCTTCAAGCTCAGGATGACTTGGTTCGCAAGATGAAAGAAGCGGCCGAGAAGCAGCTGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acagtgccatttgagatagtttaatttttgtggcacaattaattgtttgttgcagTGAGTACTCGATGCAGCTGAATGCTTCTCGGATCAAAGTTCTTCAAGCTCAAGATGACGTGATCAGTTCCATGAAAGAAGCTGCATCCAAGGAACTGTTG
aattaat putative branch site (score: 3)
atttgagatagtttaa TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcatgtgaagtatggagtgttgtgctgtgctctaaagtggcaaaaacagtgccatttgagatagtttaatttttgtggcacaattaattgtttgttgcagTGAGTACTCGATGCAGCTGAATGCTTCTCGGATCAAAGTTCTTCAAGCTCAAGATGACGTGATCAGTTCCATGAAAGAAGCTGCATCCAAGGAACTGTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
tcatgtg
- - - - - - - gagtgtt
- - - - - - - - - - - -gctgtgc
- - - - - - - - - - - - - - - - - - - - -aaaaaca
- - - - - - - - - - - - - - - - - - - - - - - - -tgccatt